Author  Title  Year  Journal  Volume,Pages 
Daniel T. Gillespie 
A General Method For Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions 
1976 
J. Chem. Physics 
22, 403434 
Daniel T. Gillespie 
Exact stochastic simulation of coupled chemical reactions 
1977 
J. Phys. Chem. 
81(25), 23402361 
M. Kohn and W. Letzkus 
A Graphtheoretical Analysis of Metablolic Regulation 
1982 
J. Theor. Biol. 
100, 293304 
D. Bray 
Intracellular signalling as a parallel distributed process 
1990 
J. Theor. Biol. 
143(2), 21531 
M. C. Kohn and D. R. Lemieux 
Identification of regulatory properties of metabolic networks by graph theoretical modeling 
1991 
J. Theor. Biol. 
150, 325 
D. L. Brutlag and A. R. Galper and D. H. Millis 
Knowledgebased simulation of DNA metabolism: prediction of enzyme action 
1991 
CABIOS 
7(1), 919 
V. N. Reddy and M. L. Mavrovouniotis and M. N. Liebman 
Petri Net Representations in Metabolic Pathways 
1993 
ISMB Proceedings 
1993, 328336 
P. D. Karp and S. M. Paley 
Representations of Metabolic Knowledge: Pathways 
1994 


D. Bray and S. Lay 
Computer Simulated Evolution of a Network of CellSignaling Molecules 
1994 
BJ 
66, 97277 
Adam Arkin and John Ross 
Computational Functions in Biochemical Reaction Networks 
1994 
Biophys. J. 
67, 560578 
Try to show signaling interactions as boolean, but fail, as only 'fuzzy' boolean 
H. H. McAdams and L. Shapiro 
Circuit Simulation of Genetic Networks 
1995 
Science 
269, 65056 
Harlie H. McAdams and Adam Arkin 
Stochastic mechanisms in gene expression 
1997 
Proc. Natl. Acad. Sci. USA 
94, 814819 
F. J. Brandenburg and M. Jünger and P. Mutzel 
Algorithmen zum automatischen Zeichnen von Graphen 
1997 
Informatik Spektrum 
27(4), 199207 
Adam Arkin and Peidong Shen and John Ross 
A Test Case of Correlation Metric Construction of a Reaction Pathway from Measurements 
1997 
Science 
277, 12751279 
Application of CMC abd MDS (multidimensional scaling) on a test case, includes short description of the computational methods, which proved surprisingly robust. 
B. N. Kholodenko and J. B. Hoek and H. V. Westerhoff and G. C. Brown 
Quantification of information transfer via cellular signal transduction pathways 
1997 
FEBS Letters 
414, 430434 
ZhiLong Xiu and AnPing Zeng and WolfDieter Deckwer 
Model analysis concerning the effects of growth rate and intracellular tryptophan level on the stability and dynamics of tryptophan biosysnthesis in bacteria 
1997 
J. Biotechnology 
58, 125140 
William M. Mounts and Michael N. Liebman 
Application of Petri Nets and Stochastic Activity Nets to Modeling Biological Pathways and Processes 
1997 
Int. J. Comp. Sim. 

W. M. Mounts and M. N. Liebman 
Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks. 
1997 
Int. J. Biol. Macromol. 
20(4), 265281 
Harley H. McAdams and Adam Arkin 
Stochastic mechanisms in gene expression 
1997 
Proc. Natl. Acad. Sci. USA 
94, 814819 
Harlie H. McAdams and Adam Arkin 
Simulation of procaryotic genetic circuits 
1998 
Annu. Rev. Biophys. Biomol. Struct. 
27, 199224 
ChiouHwa Yuh and Hamid Bolouri and Eric H. Davidson 
Genomic CisRegulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene 
1998 
Science 
279, 18961902 
Christophe H. Schilling and Bernhard O. Palsson 
The underlying pathway structure of biochemical reaction networks 
1998 
Proc. Natl. Acad. Sci. USA 
95, 41934198 
Vgl. Schuster 
R. Hofestädt and S. Thelen 
Quantitative Modeling of Biochemical Networks 
1998 
In Silico Biol. 
1, 0005 
T. TakaiIgarashi and T. Kaminuma 
A Pathway Finding System for the Cell Signaling Networks Database 
1998 
In Silico Biol. 
1, 0012 
Adam Arkin and John Ross and Harley H. McAdams 
Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage $lambda$infected textsl Escherichia coli Cells 
1998 
Genetics 
149, 16331648 
Marasu Tomita and others 
ECELL: software environment for wholecell simulation 
1998 
Bioinformatics 
15, 7284 
A. U. Igamberdiev 
Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks 
1999 
BioSystems 
50, 116 
Michael J. Fisher and Raymond C. Paton and Koichiro Matsuno 
Intracellular signalling proteins as 'smart' agents in parallel distributed processes 
1999 
BioSystems 
50, 159171 
Robert Küffner and Ralf Zimmer and Thomas Lengauer 
Pathway Analysis in Metabolic Databases via Differential Metabolic Display 
1999 
GCB 

R. Somogyi and S. Fuhrmann 
Distributivity, a general information theoretic network measure, or why the whole is more than the sum of ist parts 
1999 
Proceedings of the International Workshop on Information Processing in Cells and Tissues 

D. Thieffry and D. Romero 
The modularity of biological regulatory networks 
1999 
BioSystems 
50, 4959 
E. Selkov and others 
Mathematical simulation and analysis of cellular metabolism and regulation 
1999 
Bioinformatics 
15(9), 749758 
S. Schuster and T. Dandekar and A. D. Fell 
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering 
1999 
TIBTECH 
17, 5360 
I. M. De la Fuente 
Diversity of temporal selforganized behaviours in a biochemical system 
1999 
BioSystems 
50, 8397 
J. Schaff and L. M. Loew 
The virtual cell 
1999 
PSB 

R. S. Erb and G. S. Michaels 
Sensitivity of Biological Models to Errors in Parameter Estimates 
1999 
PSB 

E. M. Marcotte and M. Pellegrini and M. J. Thompson and T. O. Yeates and D. Eisenberg 
A combined algorithm for genomewide prediction of protein function. 
1999 
Nature 
402, 836 
Sui Huang 
Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery 
1999 
J. Mol. Med. 
77, 469480 
5000ft overview 
T. Pfeiffer and I. S'anchezValdenebro and J. C. Nuno and F. Montero and S. Schuster 
METATOOL: for studying metabolic networks 
1999 
Bioinformatics 
15(3), 251257 
Andrew Wuensche 
Classifying cellular automata a utomatically: Finding gliders, filtering, and relating spacetime patterns, attractor basins, and the Z parameter 
1999 
Complexity 
4(3), 4766 
H. L. Hartwell and J. J. Hopfield and S. Leibler and A. W. Murray 
From molecular to modular cell biology 
1999 
Nature 
402(SUPP), C47C52 
B. Schönfisch and A. de Roos 
Synchronous and asysnchronous updating in cellular automata 
1999 
BioSystems 
51, 123143 
G. Wenig and U. S. Bhalla and R. Iyengar 
Complexity in Biological Signaling Systems 
1999 
Science 
284, 9296 
E. M. Marcotte and M. Pellegrini and H. L. Ng and D. W. Rice and T. O. Yeates and D. Eisenberg 
Detecting protein function and proteinprotein interactions from genome sequences. 
1999 
Science 
285, 7513 
L. Mendoza and D. Thieffry and E. R. AlvarezBuylla 
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis 
1999 
Bioinformatics 
15(07), 593606 
T. R. Golub and D. K. Slonim and P. Tamayo and C. Huard and M. Gaasenbeek and J. P. Mesirov and H. Coller and M. L. Loh and J. R. Downing and M. A. Caligiuri and C. D. Bloomfield and E. S. Lander 
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring 
1999 
Science 
286, 531537 
seminal paper 
Ting Chen and Hongyu L. He and George M. Church 
Modeling Gene Expression with differential equations 
1999 
PSB 

interesting math 
Vassily Hatzimanikatis and Kevin H. Lee 
Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information 
1999 
Metabolic Engineering 
1, 275281 
Cool Ref about feedback cycles 
D. C. Weaver and C. T. Workman and G. D. Stromo 
Modeling regulatory networks with weight matrices 
1999 
PSB 

good 
P. D'haeseleer and S. Liang and R. Somogyi 
Gene Expression Data Analysis and Modeling 
1999 
PSB 

V. Krishnamurthy and E. V. Krishnamurthy 
Rulebased programming paradigm: a formal basis for biological, chemical and physical computation 
1999 
BioSystems 
49, 205228 
U. S. Bhalla and R. Iyengar 
Emergent Properties of Networks of Biological Signaling Pathways 
1999 
Science 
283, 381387 
I. Rojdestvenski and M. Cottam and Y.I. Park and G. Öquist 
Robustness and timescale hierarchy in biological systems 
1999 
BioSystems 
50, 7182 
Hartmann Genrich and Robert Küffner and Klaus Voss 
Executable Petri Net Models for the Analysis of Metabolic Pathways 
2000 
unpublished 

Solid application of Design/CPN to metabolic networks. 
Drew Endy and Lingchong You and Ian J. Molineux 
Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes 
2000 
Proc. Natl. Acad. Sci. USA 
97, 53755380 
Peter D. Karp 
An ontology for biological function based on molecular interactions 
2000 
Bioinformatics 
16, 269285 
Atul J. Butte and Pablo Tamayo and Donna Slonim and Todd R. Golub and Isaac S. Kohane 
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks 
2000 
Proc. Natl. Acad. Sci. USA 
97, 1218212186 
Application of the relevance network approach, together with entropy based filetring. Second paper on RelNets. 
Takako TakaiIgarashi and Tsuguchika Kaminuma 
A Pathway Finding System for the Cell Signaling Networks Database 
2000 
In Silico Biol. 
1, 980112 
Michael A. Gibson and Jehoshua Bruck 
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels 
2000 
J. Chem. Physics 
104, 18761889 
Daniel T. Gillespie 
The chemical Langevien equation 
2000 
J. Chem. Physics 
113(1), 297305 
Christopher V. Rao and Adam P. Arkin 
Control Motifs in Intracellular Regulatory Networks 
2000 


Reviews methods in network analysis: MCA, elementary flux modes. For gene regulatory nets boolean, diff. eqs and stochastic simulation. 
Ioannis Xenarios and Esteban Fernandez and Lukasz Salwinski and Xiaoqun Joyce Duan and Michael J. Thompson and Edward M. Marcotte and David Eisenberg 
DIP: The Database of Interacting Proteins: 2001 update 
2001 
Nucleic Acids Res. 
29(1), 239241 
Steven H. Strogatz 
Exploring complex networks 
2001 
Nature 
410, 268276 
A good review about the amenability of networks/dynamic systems to mathematical analysis. Either they are homogenously structured and thus can be handled statistically, or they have a complex structure, and we only can resort to topology and detailed simulation. 
Thomas Pfeiffer and Stefan Schuster and Sebastian Bonhoeffer 
Cooperation and Competition in the Evolution of ATPProducing Pathways 
2001 
Science 
292, 504506 
Cool little paper compares ATP production by slow highyield respiration and fast lowyield fermentation. With Competition (eg. for an external food source) respiration looses to fermentation. With Cooperativity (eg. multicellular organism with internalized food), respiration wins. 
H. Jeong and S. P. Mason and A.L. Barabasi and Z. N. Oltvai 
Lethality and centrality in protein networks 
2001 
Nature 
411, 4142 
Shows powerlaw for number of connections in interaction databases, and that knoking out a highly connected node has high probability to fundamentally change the network, while a random knockout will not have much effect. 
Drew Endy and Roger Brent 
Modelling cellular behaviour 
2001 
Nature 
409, 391395 
General discussion of the problem of limited data 
Christian von Mering and Roland Krause and Berend Snel and Michael Cornell and Stephen G. Oliver and Stanley Fields and Peer Bork 
Comparative assessment of largescale data sets of proteinprotein interactions 
2002 
Nature 
DOI 10.1038/750, 15 
Compares Y2H, TAP, HMSPCI, correlated mRNA, synthetic lethality and in silico genomic comparison (gene clusters, conserved operons, fusion proteins) for finding proteinprotein interaction vs. handannotated set in yeast. All methods are highly unreliable (> 50 percent error), but combinations are not. Estimate 30.000 interactions in yeast. Good references. 
E. Ravasz and A. L. Somera and D. A. Mongru and Z. N. Oltvai and A. L. Barabasi 
Hierarchical organization of modularity in metabolic networks. 
2002 
Science 
297(5586), 15515 
Hartmut Scheel and Stefan Tomiuk and Kay Hofmann 
A common protein interaction domain links two recently identified epilepsy genes 
2002 
Human Molecular Genetics 
11(15), 17571762 
Sequenceanalysis based, nice. 
Mor Peleg and Iwei Yeh and Russ B. Altman 
Modelling biological processes using workflow and Petri Net models 
2002 
Bioinformatics 
18(6) 
Daniel Hanisch and Alexander Zien and Ralf Zimmer and Thomas Lengauer 
CoClustering of Biological Networks and Gene Expression Data 
2002 
Bioinformatics 
18(Suppl 1), 145S154S 
Combinartion of network distance and expession clustering with a squashing function 
E. Demir and O. Babur and U. Dogrusoz and A. Gursoy and G. Nisanci and R. CetinAtalay and M. Ozturk 
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. 
2002 
Bioinformatics 
18(7), 9961003 
Similar my Ph.D. work on Transpath. Nice graphics. Compound graphs and Metareactions that contain subnets, too. 
Xianghong Zhou and MingChih J. Kao and Wing Hung Wong 
Transitive functional annotation by shortestpath analysis of gene expression data 
2002 
Proc. Natl. Acad. Sci. USA 
99(20), 1278312788 
Using transitive correlation to build a graph between genes. Then check for shared annotation in shortest paths between nodes in that graph, assigning shared (parental) annotation from GO. 
T. Oyama and K. Kitano and K. Satou 2 and T. Ito 
Extraction of knowledge on proteinprotein interaction by association rule discovery 
2002 
Bioinformatics 
18(5) 
Kam D. Dahlquist and Nathan Salomonis and Karen Vranizan and Steven C. Lawlor and Bruce R. Conklin 
GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways 
2002 
Nature Genetics 

Short advertisment for GenMAPP. 
Upinder S. Bhalla 
The chemical organization of signaling interactions 
2002 
Bioinformatics 
18(6) 
AnneClaude Gavin and Giulio SupertiFurga and others 
Functional organization of the yeast proteome by systematic analysis of protein complexes 
2002 
Nature 
415, 141147 
Complex identification with TAP and MALDITOF MS from 1.700 genes yielding 230 complexes, some found by multiple bait. Interesting are statistical data about complexes; finding of new complex members and assignment of function to orthologues in the matching human complexes; and proteins shared between complexes: using these a complexnetwork is constructed. (Note to me: one could see binary interactions as a complex with two members, unifying complexes and binteractions.) 